3D6N - JenaLib

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Title :   CRYSTAL STRUCTURE OF AQUIFEX DIHYDROOROTASE ACTIVATED BY ASPARTATE TRANSCARBAMOYLASE

Authors :   B. F. P. Edwards

Date :   20 May 08 (Deposition) - 20 Jan 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (6x)
Biol. Unit 2: A,B  (1x)

Keywords :   Reactor, Chamber, Pores, Internal Cavity, Hydrolase, Metal-Binding, Pyrimidine Biosynthesis, Transferase, Hydrolase-Transferase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Zhang, P. D. Martin, C. Purcarea, A. Vaishnav, J. S. Brunzelle, R. Fernando, H. I. Guy-Evans, D. R. Evans, B. F. Edwards
Dihydroorotase From The Hyperthermophile Aquifiex Aeolicus Is Activated By Stoichiometric Association With Aspartate Transcarbamoylase And Forms A One-Pot Reactor For Pyrimidin Biosynthesis.
Biochemistry V. 48 766 2009
PubMed-ID: 19128030 | Reference-DOI: 10.1021/BI801831R

Molecule 1 - DIHYDROOROTASE
	Chains	:	A
	EC Number	:	3.5.2.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PAAPYRC
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PYRC, AQ_806
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363
	Synonym	:	DHOASE

Molecule 2 - ASPARTATE CARBAMOYLTRANSFERASE
	Chains	:	B
	EC Number	:	2.1.3.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PAAPYRB
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PYRB, AQ_409
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363
	Synonym	:	ASPARTATE TRANSCARBAMYLASE, ATCASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (6x)	:	A	B
Biological Unit 2 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	FLC	2	Ligand/Ion	CITRATE ANION
2	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 12)

No.	Name	Count	Type	Full Name
1	FLC	12	Ligand/Ion	CITRATE ANION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	FLC	2	Ligand/Ion	CITRATE ANION
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:61 , HIS A:63 , ASP A:153 , ASP A:305	BINDING SITE FOR RESIDUE ZN A 423
2	AC2	SOFTWARE	HIS A:63 , ARG A:65 , ASN A:95 , ASP A:153 , GLY A:154 , HIS A:180 , HIS A:232 , ASN A:278 , ASP A:305 , ALA A:307 , HIS A:309 , PRO A:322 , GLY A:323	BINDING SITE FOR RESIDUE FLC A 424
3	AC3	SOFTWARE	THR B:48 , ARG B:97 , HIS B:126 , ARG B:159 , ARG B:213 , GLY B:251	BINDING SITE FOR RESIDUE FLC B 292

(no "SS Bond" information available for 3D6N)

Asymmetric Unit

No.	Residues
1	Asp A:66	-	Pro A:67
2	Asn A:97	-	Pro A:98
3	Asp A:153	-	Gly A:154
4	Asn A:278	-	Pro A:279
5	Phe B:103	-	Pro B:104

(no "SAP(SNP)/Variant" information available for 3D6N)

Asymmetric Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CARBAMOYLTRANSFERASE	PS00097	Aspartate and ornithine carbamoyltransferases signature.	PYRB_AQUAE	41-48	1	B:41-48
2	DIHYDROOROTASE_1	PS00482	Dihydroorotase signature 1.	PYRC_AQUAE	59-67	1	A:59-67
3	DIHYDROOROTASE_2	PS00483	Dihydroorotase signature 2.	PYRC_AQUAE	303-314	1	A:303-314

Biological Unit 1 (3, 18)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CARBAMOYLTRANSFERASE	PS00097	Aspartate and ornithine carbamoyltransferases signature.	PYRB_AQUAE	41-48	6	B:41-48
2	DIHYDROOROTASE_1	PS00482	Dihydroorotase signature 1.	PYRC_AQUAE	59-67	6	A:59-67
3	DIHYDROOROTASE_2	PS00483	Dihydroorotase signature 2.	PYRC_AQUAE	303-314	6	A:303-314

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CARBAMOYLTRANSFERASE	PS00097	Aspartate and ornithine carbamoyltransferases signature.	PYRB_AQUAE	41-48	1	B:41-48
2	DIHYDROOROTASE_1	PS00482	Dihydroorotase signature 1.	PYRC_AQUAE	59-67	1	A:59-67
3	DIHYDROOROTASE_2	PS00483	Dihydroorotase signature 2.	PYRC_AQUAE	303-314	1	A:303-314

(no "Exon" information available for 3D6N)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:422
 aligned with PYRC_AQUAE | O66990 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:422
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420  
           PYRC_AQUAE     1 MLKLIVKNGYVIDPSQNLEGEFDILVENGKIKKIDKNILVPEAEIIDAKGLIVCPGFIDIHVHLRDPGQTYKEDIESGSRCAVAGGFTTIVCMPNTNPPIDNTTVVNYILQKSKSVGLCRVLPTGTITKGRKGKEIADFYSLKEAGCVAFTDDGSPVMDSSVMRKALELASQLGVPIMDHCEDDKLAYGVINEGEVSALLGLSSRAPEAEEIQIARDGILAQRTGGHVHIQHVSTKLSLEIIEFFKEKGVKITCEVNPNHLLFTEREVLNSGANARVNPPLRKKEDRLALIEGVKRGIIDCFATDHAPHQTFEKELVEFAMPGIIGLQTALPSALELYRKGIISLKKLIEMFTINPARIIGVDLGTLKLGSPADITIFDPNKEWILNEETNLSKSRNTPLWGKVLKGKVIYTIKDGKMVYKD 422
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeeehhhheee..eeeee..eeeeee........eeee....eeee.eeeeee...........hhhhhhhhhhhh.eeeeee.........hhhhhhhhhhhhhhhh..eeee....hhhhh.....hhhhhhhhh............hhhhhhhhhhhhhhh...eee...........ee.hhhhhhhh..eehhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhh....eeeeehhhhhhh..hhhhhhhhhhh......hhhhhhhhhhhhhh....ee.......hhhhh.hhhhh........hhhhhhhhhhhh...hhhhhhhh.hhhhhhhhh.............eeeeeeeeeee..................eeeeeeeeeee..eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------DIHYDROOR-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DIHYDROOROTA------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d6n A   1 MLKLIVKNGYVIDPSQNLEGEFDILVENGKIKKIDKNILVPEAEIIDAKGLIVCPGFIDIHVHLRDPGQTYKEDIESGSRCAVAGGFTTIVCMPNTNPPIDNTTVVNYILQKSKSVGLCRVLPTGTITKGRKGKEIADFYSLKEAGCVAFTDDGSPVMDSSVMRKALELASQLGVPIMDHCEDDKLAYGVINEGEVSALLGLSSRAPEAEEIQIARDGILAQRTGGHVHIQHVSTKLSLEIIEFFKEKGVKITCEVNPNHLLFTEREVLNSGANARVNPPLRKKEDRLALIEGVKRGIIDCFATDHAPHQTFEKELVEFAMPGIIGLQTALPSALELYRKGIISLKKLIEMFTINPARIIGVDLGTLKLGSPADITIFDPNKEWILNEETNLSKSRNTPLWGKVLKGKVIYTIKDGKMVYKD 422
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420

Chain B from PDB  Type:PROTEIN  Length:291
 aligned with PYRB_AQUAE | O66726 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:291
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290 
           PYRB_AQUAE     1 MRSLISSLDLTREEVEEILKYAKEFKEGKEETIKASAVLFFSEPSTRTRLSFEKAARELGIETYLVSGSESSTVKGESFFDTLKTFEGLGFDYVVFRVPFVFFPYKEIVKSLNLRLVNAGDGTHQHPSQGLIDFFTIKEHFGEVKDLRVLYVGDIKHSRVFRSGAPLLNMFGAKIGVCGPKTLIPRDVEVFKVDVFDDVDKGIDWADVVIWLRLQKERQKENYIPSESSYFKQFGLTKERFEKVKLYMHPGPVNRNVDIDHELVYTEKSLIQEQVKNGIPVRKAIYKFLWT 291
               SCOP domains d3d6nb1 B:1-142 automated matches                                                                                                             d3d6nb2 B:143-291 automated matches                                                                                                                   SCOP domains
               CATH domains 3d6nB01 B:1-125,B:270-291  [code=3.40.50.1370, no name defined]                                                              3d6nB02 B:126-269  [code=3.40.50.1370, no name defined]                                                                                         3d6nB01                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhh........eeeeee...hhhhhhhhhhhhhhh..eeeeee..........hhhhhhhhhhhh...eeeeee......hhhhhhh...eeeeeee....hhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhh..eeeee.hhhhh..hhhhh.eee..hhhhhhhhh.eeee....hhhhhh....hhhhhhhhhh.hhhhhh....ee...........hhhhh.....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------CARBAMOY--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d6n B   1 MRSLISSLDLTREEVEEILKYAKEFKEGKEETIKASAVLFFSEPSTRTRLSFEKAARELGIETYLVSGSESSTVKGESFFDTLKTFEGLGFDYVVFRVPFVFFPYKEIVKSLNLRLVNAGDGTHQHPSQGLIDFFTIKEHFGEVKDLRVLYVGDIKHSRVFRSGAPLLNMFGAKIGVCGPKTLIPRDVEVFKVDVFDDVDKGIDWADVVIWLRLQKERQKENYIPSESSYFKQFGLTKERFEKVKLYMHPGPVNRNVDIDHELVYTEKSLIQEQVKNGIPVRKAIYKFLWT 291
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: ATC-like (129)

Superfamily: Aspartate/ornithine carbamoyltransferase (122)

Family: automated matches (35)

Protein domain: automated matches (35)

Aquifex aeolicus [TaxId: 63363] (2)

1a	d3d6nb1	B:1-142
1b	d3d6nb2	B:143-291

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1370, no name defined] (91)

Aquifex aeolicus. Organism_taxid: 63363. (1)

1a	3d6nB01	B:1-125,B:270-291
1b	3d6nB02	B:126-269

(no "Pfam Domain" information available for 3D6N)

Asymmetric Unit(hide GO term definitions)

Chain A (PYRC_AQUAE | O66990)

molecular function
	GO:0004151	dihydroorotase activity	Catalysis of the reaction: (S)-dihydroorotate + H(2)O = N-carbamoyl-L-aspartate + H(+).
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016810	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
	GO:0016812	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides	Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a cyclic amide.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0044205	'de novo' UMP biosynthetic process	The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD(+) or oxygen.
	GO:0006221	pyrimidine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

Chain B (PYRB_AQUAE | O66726)

molecular function
	GO:0016597	amino acid binding	Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
	GO:0004070	aspartate carbamoyltransferase activity	Catalysis of the reaction: L-aspartate + carbamoyl phosphate = N-carbamoyl-L-aspartate + H(+) + phosphate.
	GO:0016743	carboxyl- or carbamoyltransferase activity	Catalysis of the transfer of a carboxyl- or carbamoyl group from one compound (donor) to another (acceptor).
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0044205	'de novo' UMP biosynthetic process	The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD(+) or oxygen.
	GO:0006207	'de novo' pyrimidine nucleobase biosynthetic process	The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
	GO:0006520	cellular amino acid metabolic process	The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
	GO:0006221	pyrimidine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	GO:0009220	pyrimidine ribonucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a pyrimidine ribonucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	GO:0000050	urea cycle	The sequence of reactions by which arginine is synthesized from ornithine, then cleaved to yield urea and regenerate ornithine. The overall reaction equation is NH3 + CO2 + aspartate + 3 ATP + 2 H2O = urea + fumarate + 2 ADP + 2 phosphate + AMP + diphosphate.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Cis Peptide Bonds
		Asn A:278 - Pro A:279	[ RasMol ]
		Asn A:97 - Pro A:98	[ RasMol ]
		Asp A:153 - Gly A:154	[ RasMol ]
		Asp A:66 - Pro A:67	[ RasMol ]
		Phe B:103 - Pro B:104	[ RasMol ]

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	PYRB_AQUAE \| O66726	:	4bjh
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Description

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